gtonkinhill / panstripeLinks
post processing of bacterial pangenome gene presence/absence matrices
☆60Updated 6 months ago
Alternatives and similar repositories for panstripe
Users that are interested in panstripe are comparing it to the libraries listed below
Sorting:
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Updated last year
- A tool for removing redundant genomes from a set of assemblies☆76Updated 2 years ago
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆52Updated last month
- whole genome MLST analysis☆46Updated 2 months ago
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆74Updated last year
- Reorients assembled microbial sequences☆125Updated last week
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆73Updated 2 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆47Updated 2 years ago
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆59Updated 4 months ago
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆49Updated 2 months ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆34Updated 2 years ago
- Gene Absence Presence Identification tool.☆27Updated 5 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆62Updated this week
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆80Updated last year
- a collection of scripts for organising bacterial genomes by species☆77Updated 3 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆30Updated 10 months ago
- Small utility script to submit genomes to PHASTER for phage detection☆25Updated 3 years ago
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆42Updated 4 years ago
- Bifrost graph gene caller.☆96Updated 11 months ago
- GTDB taxonomy taxdump files with trackable TaxIds☆56Updated 4 months ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated last month
- Prediction of prophages from bacterial genomes☆79Updated 2 months ago
- Ley Lab MetaGenome Profiler DataBase generator☆50Updated 2 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- ☆53Updated last month
- Graph-based assembly phasing☆86Updated 4 months ago
- Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasm…☆51Updated 4 years ago
- A python library for predicting phage lifestyle based on genome sequence☆38Updated 2 years ago